Recombination between bacteriophage Lambda and its host Escherichia coli (site-specific recombination) is effected by a pair of reciprocal strand exchanges that occur within special sequences called attachment sites. We have previously shown that base substitution mutations in the central segment of an attachment site interfere with recombination by preventing homologous pairing betwen the mutated site and its wild type partner. Our recent results suggest that the same mutation also prevents conversion of a Holliday structure -- an X-shaped DNA molecule that is a postulated intermediate in recombination -- to recombinant products. It therefore appears possible that a direct interaction between homologous regions is also necessary for this step in the reaction. We previously showed that endonuclease I of bacteriophage T7 cleaves Holliday structures. We have now extended our original observation, made with a short cruciform DNA substrate, to several other substrates, including Holliday structures formed from phage Lambda attachment sites. We have made the surprising observation that introduction of a base substitution mutation into the central region of the Lambda Holliday structure affects the symmetry of cleavage: instead of obtaining all four products in equal yield, only two products are obtained. It appears likely that the effect of the mutation is to limit the extent of branch migration of the Holliday structure. We have discovered that HK022, a temperate coliphage related to Lambda produces a protein that causes RNA polymerase to terminate transcription when it encounters specific sequences in the early region of the phage Lambda chromosome. Termination occurs at or near sequences called nut sites and requires host encoded proteins called nus factors. Nut sites and nus factors are also required for a contrasting process: antitermination of transcription by the Lambda N protein. It is of considerable interest that termination and antitermination of transcription appear to have mechanistic steps in common.